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OmicsPLS specifications

Information


Unique identifier OMICS_32446
Name OmicsPLS
Alternative name O2PLS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.0
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/OmicsPLS_1.1.0.tar.gz
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Said el Bouhaddani

Publication for OmicsPLS

OmicsPLS citations

 (51)
library_books

Maize Stem Response to Long Term Attack by Sesamia nonagrioides

2018
Front Plant Sci
PMCID: 5925969
PMID: 29740463
DOI: 10.3389/fpls.2018.00522

[…] In an effort to integrate the metabolomics and transcriptomic data, we performed an O2PLS analysis. This analysis indicated that two groups of genes had the highest impact on the metabolome. The first group included genes involved in primary metabolism and plant growth that were down […]

library_books

The Arabidopsis thaliana Knockout Mutant for Phytochelatin Synthase1 (cad1 3) Is Defective in Callose Deposition, Bacterial Pathogen Defense and Auxin Content, But Shows an Increased Stem Lignification

2018
Front Plant Sci
PMCID: 5786554
PMID: 29403524
DOI: 10.3389/fpls.2018.00019

[…] ubled their relative levels from wild-type to cad1-3 or vice versa.The distinct clusters of metabolites from wild-type and cad1-3 plants (shoots and roots) along the first two principal components in O2PLS-DA analysis (Supplementary Figure ) show the effect of AtPCS1 on the secondary metabolism. The identified metabolite list is reported in Supplementary Table .In general, both indole and aliphati […]

library_books

A quantitative multimodal metabolomic assay for colorectal cancer

2018
BMC Cancer
PMCID: 5755335
PMID: 29301511
DOI: 10.1186/s12885-017-3923-z

[…] h has shown to be sufficiently reliable for the purpose of multivariate statistical analyses, including OPLS-DA [, ].To assess the performance of supervised multivariate models, including OPLS-DA and O2PLS-DA, R2Y and Q2Y scores were used for measurement of the dataset variance covered by the model, and the predictability of the model in 7-fold cross-validation []. Models with the difference of mo […]

library_books

A multi omics approach reveals function of Secretory Carrier Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees

2018
BMC Genomics
PMCID: 5753437
PMID: 29298676
DOI: 10.1186/s12864-017-4411-1

[…] c lines from the five different omics platforms (transcriptomic, proteomic, GC-MS metabolomic, LC-MS metabolomic and Py-GC/MS metabolomic) and compared to the wild type. OnPLS [, ] is an extension of O2PLS [, ], and suitable for simultaneous analysis of more than two blocks of data or, as in our case, data from more than two platforms. It separates each data block into three parts: one where the d […]

library_books

Amyloid β42 peptide is toxic to non neural cells in Drosophila yielding a characteristic metabolite profile and the effect can be suppressed by PI3K

2017
PMCID: 5703620
PMID: 29141953
DOI: 10.1242/bio.029991

[…] CA) are highly informative when analyzing differences in metabolite profiles, other effects may hide the variation of interest. Thus, orthogonal projection to latent structures discriminant analysis (O2PLS-DA) () was used to focus the analysis on the variation that separates the different combinations of protein expression and age. The O2PLS-DA models were carried out on Pareto-scaled data. They w […]

library_books

Alzheimer's brains show inter related changes in RNA and lipid metabolism

2017
PMCID: 5560656
PMID: 28630030
DOI: 10.1016/j.nbd.2017.06.008

[…] over 100 quantifiable lipid metabolites and enabled comparison to pure standards as a basis for analysis. Comparing the complete lipidomic profiles (9312 peaks) by supervised multivariate statistics (O2PLS-DS, a) provided an unambiguous classification of 3 distinct groups, namely early AD (eAD), late AD (lAD) and the healthy controls and NDWP groups, which were only partially separated, indicating […]

Citations

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OmicsPLS institution(s)
Department of Biomedical Data Sciences, LUMC, Leiden, The Netherlands; Department of Biostatistics and Research Support, UMC Utrecht, Utrecht, The Netherlands; Delft Institute of Applied Mathematics, EEMCS, Delft, Delft,The Netherlands; Department of Statistics, University of Leeds, Leeds, UK; Genos Glycobiology Laboratory, Zagreb, Croatia; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
OmicsPLS funding source(s)
Supported by the European Union’s Seventh Framework Programme (FP7-Health-F5-2012) under grant agreement number 305280.

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